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PubMed2006

Bioremediation of halogenated compounds: comparison of dehalogenating bacteria and improvement of catalyst stability.

Five bacterial strains were compared for halogenated compounds conversion in aqueous media. Depending on the strain, the optimal temperature for dehalogenase activity of resting cells varied from 30 to 45 degrees C, while optimal pH raised from 8.4 to 9.0. The most effective dehalogenase activity for 1-chlorobutane conversion was detected with Rhodococcus erythropolis NCIMB13064 and Escherichia coli BL21 (DE3) (DhaA). The presence of 2-chlorobutane or propanal in the aqueous media could inhibit the 1-chlorobutane transformation.

Biodegradation, Environmental↗

PubMed2006

Interaction of metabolites with R. rhodochrous during the biodegradation of di-ester plasticizers.

The commonly used plasticizers di-ethylhexyl phthalate (DEHP) and di-ethylhexyl adipate (DEHA) are known to partially degrade in the presence of soil microorganisms, such as Rhodococcus rhodochrous, releasing persistent and toxic metabolites. The metabolites adipic acid and 2-ethylhexanol were both shown to inhibit growth of the degrading microbe. 2-Ethylhexanol enhanced the activity of ethanol dehydrogenase - an enzyme involved in its metabolism - but the activity of this enzyme was inhibited by adipic acid. The metabolite usually seen in the highest concentrations - 2-ethylhexanoic acid - did not exhibit any evidence of inhibition. It was shown that the high concentration of this metabolite was due to the inability of R. rhodochrous to degrade it. Comparisons with other small carboxylic acids supported the argument that the ethyl branch was the reason for the resistance of 2-ethylhexanoic acid to degradation. The hydrophobicity of the cell surface was shown to be a factor in plasticizer degradation. The primary carbon source could be either water-soluble or hydrophobic and a hydrophobic substrate led to a cell surface that attracted the plasticizer and facilitated degradation. The most hydrophobic of the plasticizers, DEHP, was particularly sensitive to this effect.

Adipates↗

PubMed2006

Seroepidemiological survey of Rhodoccocus equi infection in asymptomatic horses from Bursa, Izmir and Istanbul provinces, Turkey.

In order to assess the Rhodococcus equi infection in three provinces of Turkey (Bursa, Izmir and Istanbul), 696 sera from healthy foals and adult horses were tested by indirect ELISA using a R. equi reference strain (ATCC 6939) as antigen. 103 sera (14.80%) with titres >0.646 resulted positive. Seroprevalence was significantly higher (P=0.0053) in male than in female horses of Istanbul province, although higher antibody titres (mean value) were observed in the female group of Bursa and Izmir provinces with differences estimated between provinces (P=0.0002). Seroprevalence was correlated with age: foals aged less than 1 year (P<10(-4)) and horses from 5 to 10 years old (P=0.018) resulted more infected in Bursa and Izmir provinces. Our findings indicate that R. equi infection actually occurs in all investigated provinces, suggesting the importance of serological survey to diagnose the infection and to prevent the zoonotic risk.

Actinomycetales Infections↗

PubMed2005

Degradation of polycyclic aromatic hydrocarbons by a bacterial consortium enriched from mangrove sediments.

The biodegradability of a polycyclic aromatic hydrocarbons (PAHs) mixture consisted of fluorene (Fl), phenanthrene (Phe) and pyrene (Pyr) by a bacterial consortium enriched from mangrove sediments under sediment-free and sediment slurry conditions was investigated. The enriched consortium made up of three bacterial strains, namely Rhodococcus sp., Acinetobacter sp. and Pseudomonas sp., had a good PAH degradation capability with 100% degradation of Fl and Phe in sediment-free liquid medium after 4 weeks of growth. The Fl and Phe degradation percentages in sediment slurry were higher than that in liquid medium. Autochthonous microorganisms in sediments also possessed satisfactory PAH degradation capability and all three PAHs were almost completely degraded after 4 weeks of growth. Bioaugumentation (inoculation of the enriched consortium to sediments) showed a positive effect on PAH biodegradation after 1 week of growth. Complete biodegradation of pyrene took longer time than that for Fl and Phe, indicating the enriched bacterial consortium had preference to utilize low-molecular weight PAHs.

Acinetobacter↗

PubMed2005

Colonization of surfaces by phenolic compounds utilizing microorganisms.

The aim of the present study is to determine optimal adhesive interaction of phenolic compounds utilizing Candida maltosa and Rhodococcus erythropolis when adhering to kaolin, silicone, synthetic foil (Steriking R40) and fluorinated silicones, comparing cell and support surface hydrophobicity. In parallel, the interfering effect of detergents was investigated. Data obtained show that the less hydrophobic supports display high initial cell adhesion when contacted with the cell type with a lower surface hydrophobicity (yeast cell) but most stable yeast biofilms are those formed on highly hydrophobic fluorinated silicones. On the other hand, support hydrophobicity has no effect on bacterial cell detachment; however, bacterial biofilms are denser when growing on more hydrophobic supports. Both detergents interfere (independently on the cell type) with the early and late phases of biofilm development.

Bacterial Adhesion↗

PubMed2005

Chemical and biochemical transformations of 5-ethoxycarbonyl-5-phenyl-2-isoxazolines.

The salts, 2-methyl-5,5-disubstituted 4,5-dihydroisoxazolium methylsulfates comprising various substituents at the C-3 carbon atom were subjected to transformations. The structure of applied compounds permitted to monitor the effect of this factor on the transformation course of the 2-isoxazoline ring. The nucleophilic addition of cyanide anion to the selected salts enabled the obtaining of a next heterocyclic system of changed physicochemical and biological properties in comparison to the starting 2-isoxazolines. The diastereoselective hydrolysis of the cyanide group in 2-isoxazolidines by the bacteria strain Rhodococcus rhodochrous PCM 909 leads to the obtaining of a racemic mixture of the trans-hydroxyacid. The introduction of new functional groups into the heterocyclic ring made these compounds attractive objects for further chemical and microbial transformations and to study their biological activity.

Anti-Infective Agents↗

PubMed2005

Analysis of the domain properties of the novel cytochrome P450 RhF.

The properties of the heme, flavin mononucleotide (FMN) and FeS domains of P450 RhF, from Rhodococcus sp. NCIMB 9784, expressed separately and in combination are analysed. The nucleotide preference, imidazole binding and reduction potentials of the heme and FMN domains are unaltered by their separation. The intact enzyme is monomeric and the flavin is confirmed to be FMN. The two one-electron reduction potentials of the FMN are -240 and -270 mV. The spectroscopic and thermodynamic properties of the FeS domain, masked in the intact enzyme, are revealed for the first time, confirming it as a 2Fe-2S ferredoxin with a reduction potential of -214 mV.

Base Sequence↗

PubMed2005

Polymerase chain reaction for identification of aldoxime dehydratase in aldoxime- or nitrile-degrading microorganisms.

We developed a molecular screening procedure using Southern hybridization and polymerase chain reaction (PCR) to identify aldoxime dehydratase (Oxd) encoding genes (oxds) among 14 aldoxime- or nitrile-degrading microorganisms. When an oxd gene of Rhodococcus erythropolis N-771 was used as a probe, positive hybridization signals were seen with the chromosomal DNA of eight strains, suggesting that these strains have similar oxd genes to R. erythoropolis N-771. By analyzing the PCR-amplified fragments with degenerate consensus primers, the occurrence of homologous Oxd coexisting with Fe-containing NHase in the active eight strains was demonstrated coinciding with the results of Southern hybridization. Whole length of oxd gene was cloned as an example from one of the positive strains, Pseudomonas sp. K-9, sequenced, and expressed in E. coli. Analysis of the primary structure of the protein (OxdK) encoded by the oxd gene of Pseudomonas sp. K-9 led to identify an Oxd having a new primary structure. Thus, the PCR-based analysis of oxd gene is a useful tool to detect and analyze the "aldoxime-nitrile pathway" in nature, since Oxd is the key enzyme for the pathway.

Amino Acid Sequence↗

PubMed2005

A chemoenzymatic route to mannosamine derivatives bearing different N-acyl groups.

The chemoenzymatic route to 2-deoxy-2-propionamido-D-mannose (1b), 2-butyramido-2-deoxy-D-mannose (2b) and 2-deoxy-2-phenylacetamido-D-mannose (3b) involved N-acylation of 2-amino-2-deoxy-D-glucose followed by alkaline C-2 epimerization and selective microbial removal of the epimers with gluco-configuration. The latter step employed whole cells of Rhodococcus equi A4 able to degrade 2-deoxy-2-propionamido-D-glucose (1a), 2-butyramido-2-deoxy-D-glucose (2a) and 2-deoxy-2-phenylacetamido-D-glucose (3a) but inactive towards the corresponding manno-isomers. The metabolism of the gluco-isomers probably involved phosphorylation and subsequent deacylation. 2-Acetamido-2-deoxy-6-O-phospho-D-glucose amidohydrolase [EC 3.5.1.25] but not 2-acetamido-2-deoxy-D-glucose amidohydrolase was detected in the cell extract, the former enzyme being partially purified (15.8-fold with an overall yield of 18.1% and a specific activity of 0.95 units mg-1 protein). According to SDS-PAGE electrophoresis, gel filtration and mass spectrometry, the enzyme was a monomer with an apparent molecular mass of approximately 42 kDa. The optimum temperature and pH of the enzyme were 60 degrees C and 8.0-9.0, respectively. 2-Acetamido-2-deoxy-6-O-phospho-D-glucose and 2-acetamido-2-deoxy-6-O-sulfo-D-glucose but not 2-acetamido-2-deoxy-1-O-phospho-D-glucose or 2-acetamido-2-deoxy-D-glucose were substrates of the enzyme. Its activity was slightly inhibited by the addition of 1 mM Al3+, Ca2+, Co2+, Cu2+, Mn2+ or Zn2+ and activated by 1 mM Mg2+. The concentrated enzyme is highly stable at 4 degrees C in the presence of 0.1 M ammonium sulfate.

Acylation↗

PubMed2006

Fermentation reactor coupled with capillary electrophoresis for on-line bioprocess monitoring.

In this paper, a filter probe integrated into a computerized pneumatic sampler for capillary electroseparations was developed for an on-line monitoring of bioprocesses. The optimization of the performance of the coupled system was done by using a response surface modeling and three-level two-factor design. The resolution was found to be the most important parameter influencing the performance of an on-line analysis of the microbial metabolism. For the on-line analysis the migration time and detection limit were also found to be important parameters. Different parameters were combined by using an overall desirability function to find optimum conditions for all parameters. The equipment with an optimized separation protocol was used to monitor the bioaccumulation of Cu, Zn, Co and Cd (with detection limits 0.46, 0.37, 1.2, 0.84 mM correspondingly) by the Rhodococcus sp. bacteria isolated from the highly polluted technogenic soil of northeastern Estonia during a 2-week experiment.

Amino Acids↗

PubMed2003

Analysis of bacterial DNA patterns--an approach for controlling biotechnological processes.

Optimisation of biotechnological processes catalysed by microbial cells requires detailed information about operational limits of the single cells. Their performance is correlated with distinct physiological states. We related these states to cell cycle events, which were found to proceed extremely diversely in different bacterial strains. Characteristic DNA patterns were found flow cytometrically, depending on the type of strain, substrates and growth conditions involved; this information can be used for the development of control strategies of bioprocesses, although some skill is required. Four bacterial strains (the Gram-negative strains Acinetobacter calcoaceticus 69-V, Ralstonia eutropha JMP 134, Ochrobactrum anthropi K2-14 and the Gram-positive strain Rhodococcus erythropolis K2-3) were grown in mono- and mixed cultures on different substrates, and analysed regarding their proliferation behaviour. The resulting DNA distribution patterns provided three types of valuable information. First, correlation of proliferation activity with the appearance of a major part of cells within the C(2) stage of the cell cycle is a strain-specific feature. Second, bacteria usually maintain more than one chromosome under limiting growth conditions: DNA replication is completed in such cases, but cell division fails. Third, high growth rates are associated with uncoupled DNA synthesis. Its general initiation might be genetically determined in the first place, but it is promoted by optimal growth conditions and the presence of substrates that can be metabolised at high rates, thereby allowing substantial amounts of carbon, other nutrients and energy to be used exclusively for DNA synthesis.

Biotechnology↗

PubMed2005

Immobilization of hydrocarbon-oxidizing bacteria in poly(vinyl alcohol) cryogels hydrophobized using a biosurfactant.

A simple biosurfactant-based hydrophobization procedure for poly(vinyl alcohol) (PVA) cryogels was developed allowing effective immobilization of hydrocarbon-oxidizing bacteria. The resulting partially hydrophobized PVA cryogel granules (granule volume 5 microl) contained sufficient number (6.5 x 10(3)) of viable bacterial cells per granule, possessed high mechanical strength and spontaneously located at the interface in water-hydrocarbon system. Such interfacial location of PVA granules allowed high contact of immobilized biocatalyst with hydrophobic substrate and water phase, thus providing bacterial cells with mineral and organic nutrients. As a result, n-hexadecane oxidation efficiency of 51% after 10-day incubation was achieved using immobilized biocatalyst. PVA cryogels with increased hydrophobicity can be used for immobilization of bacterial cultures performing oxidative transformations of water-immiscible organic compounds. Immobilization of in situ biosurfactant producing Rhodococcus bacteria into PVA cryogel is discussed. PVA cryogel granules with entrapped alkanotrophic rhodococcal cells were stable after 10-month storage at room temperature.

Alkanes↗

PubMed2005

Characterization of microorganisms isolated from lignite excavated from the Záhorie coal mine (southwestern Slovakia).

Microorganisms were isolated from lignite freshly excavated in the Záhorie coal mine (southwestern Slovakia) under conditions excluding contamination with either soil or air-borne microorganisms. The isolates represented both Prokarya and Eukarya (fungi). All were able to grow on standard media, although some microorganisms were unstable and became extinct during storage of coal samples. Bacteria belonged to the genera Bacillus, Staphylococcus, and Rhodococcus, according to both morphological criteria and ITS sequences. Several bacterial isolates were resistant to antibiotics. The presence of anaerobic bacteria was also documented, although they have not yet been identified. Fungal isolates were typified by using their ITS sequences. They belonged to the genera Trichoderma (Hypocrea), Penicillium, Epicoccum, Metarhizium (Cordyceps), and Cladosporium. Several fungi produced compounds with antibiotic action against standard bacterial strains. The evidence for the presence of microorganisms in native lignite was obtained by means of fluorescence microscopy, scanning electron microscopy, and electron microprobe analysis. Results demonstrated that microorganisms were able to survive in the low-rank coal over a long time period.

Anti-Bacterial Agents↗

PubMed2003

Purification and characterization of the aromatic desulfinase, 2-(2'-hydroxyphenyl)benzenesulfinate desulfinase.

2-(2(')-Hydroxyphenyl)benzenesulfinate desulfinase (HPBS desulfinase) catalyzes the cleavage of the carbon-sulfur bond of 2-(2(')-hydroxyphenyl)benzenesulfinate (HPBS) to form hydroxybiphenyl and sulfite. This is the final step in the desulfurization of dibenzothiophene, the organosulfur compound used to study biodesulfurization of petroleum middle distillate. HPBS desulfinase was purified 1600-fold from Rhodococcus IGTS8. The purification was monitored using a spectrofluorimetric assay and SDS-PAGE. The pI of HPBS desulfinase is 5.6, the temperature optimum is 35 degrees C, and the pH optimum is 7.0. HPBS desulfinase has a K(m) of 0.90+/-0.15 microM and a k(cat) of 1.3+/-0.07 min(-1). Several analogs were tested for their ability to act as substrates or inhibitors of HPBS desulfinase. No alternative substrates and very few inhibitors were identified. HPBS desulfinase activity decreases in the presence of Cu(2+) and Zn(2+), while no metals significantly enhance enzyme activity. HPBS desulfinase is susceptible to tyrosine, tryptophan, and cysteine specific modification agents.

Cells, Cultured↗

PubMed2003

Motif CXCC in nitrile hydratase activator is critical for NHase biogenesis in vivo.

Nitrile hydratase (NHase) activator from Rhodococcus sp. N-771 is required for NHase functional expression. The motif 73CXCC76 in the NHase activator sequence was here revealed to be vital for its function by site-directed mutagenesis. All three substitutions of the cysteines by serines resulted in a much lower level of expression of active NHase. Furthermore, interaction between NHase activator and NHase was detected and the critical role of NHase activator was not exhibited in the cysteine oxidization process of NHase. These findings suggest NHase activator mainly participates in iron trafficking in NHase biogenesis as an iron type metallochaperone.

Amino Acid Motifs↗

PubMed1997

Highly efficient control of iron-containing nitrile hydratases by stoichiometric amounts of nitric oxide and light.

The reaction of two iron-containing nitrile hydratases (NHase) with NO has been studied: NHase from Rhodococcus sp. R312, which is probably similar to the photosensitive N771 NHase, and the new NHase from Comamonas testosteroni NI1 whose aminoacid sequence is quite different from those of BR312 and N771 NHases. Both enzymes are equally inactivated after addition of stoichiometric amounts of NO added as an anaerobic solution or produced in situ under physiological conditions by a rat brain NO-synthase. Both enzymes are reactivated by photoirradiation, and two cycles of NO inactivation/photoactivation can be performed without significant loss of activity. Both iron-containing NHases have a high affinity for NO, similar to that of methemoglobin.

Animals↗

PubMed1997

Dissecting the assembly pathway of the 20S proteasome.

Proteasomes reach their mature active state via a complex cascade of folding, assembly and processing events. The Rhodococcus proteasome offers a means to dissect the assembly pathway and to characterize intermediates; its four subunits (alpha1, alpha2, beta1, beta2) assemble efficiently in vitro with any combination of alpha and beta. Assembly studies with wild-type and N-terminally truncated beta-subunits in conjunction with refolding studies allowed to define the role of the propeptide which is two-fold: It supports the initial folding of the beta-subunits and it promotes the maturation of the holoproteasomes.

Cloning, Molecular↗

PubMed1998

XAS characterization of the active sites of novel intradiol ring-cleaving dioxygenases: hydroxyquinol and chlorocatechol dioxygenases.

The intradiol cleaving dioxygenases hydroxyquinol 1,2-dioxygenase (HQI,20) from Nocardiodes simplex 3E, chlorocatechol 1,2-dioxygenase (CIC1,20) from Rhodococcus erythropolis ICP, and their anaerobic substrate adducts (hydroxyquinol-HQ1,20 and 4-chlorocatechol-CIC1,20) have been characterized through X-ray absorption spectroscopy. In both enzymes the iron(III) is pentacoordinated and the distance distribution inside the Fe(III) first coordination shell is close to that already found in the extensively characterized protocatechuate 3,4-dioxygenase. The coordination number and the bond lengths are not significantly affected by the substrate binding. Therefore it is confirmed that the displacement of a protein donor upon substrate binding has to be considered a general step valid for all intradiol dioxygenases.

Actinomycetales↗